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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ), 'gf_id' => 'HOM05D001131', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001131' ), 'data_identifier' => 'HOM05D001131', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001131', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '545', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p39760' => 'bna', 'A03p58720' => 'bna', 'A05p19120' => 'bna', 'A05p33210' => 'bna', 'A08p02370' => 'bna', 'Aa31LG10G2750' => 'aar', 'Aa31LG2G21410' => 'aar', 'Aa31LG8G3470' => 'aar', 'Actinidia09444' => 'ach', 'Actinidia21705' => 'ach', 'Actinidia32701' => 'ach', 'Actinidia39139' => 'ach', 'Actinidia39140' => 'ach', 'Ah.01g021930' => 'amhyb', 'Ah.01g021940' => 'amhyb', 'Ah.01g021950' => 'amhyb', 'Ah.01g021960' => 'amhyb', 'Ah.01g021970' => 'amhyb', 'Ah.02g128740' => 'amhyb', 'Ah.09g230700' => 'amhyb', 'AL1G60230' => 'aly', 'AL3G29080' => 'aly', 'AL4G34500' => 'aly', 'AL4G34540' => 'aly', 'AL7G23330' => 'aly', 'Aqoxy271s001' => 'aox', 'Aqoxy3G01772' => 'aox', 'Aqoxy5G02997' => 'aox', 'Aqoxy7G01451' => 'aox', 'Aqoxy7G01452' => 'aox', 'Aqoxy7G01453' => 'aox', 'Aqoxy7G01455' => 'aox', 'Aqoxy7G03882' => 'aox', 'arahy.Tifrunner.gnm1.ann1.646R5W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I6Q85W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.LR2U11' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X7S7J8' => 'arhy', 'AT1G52140' => 'ath', 'AT3G16330' => 'ath', 'AT4G29110' => 'ath', 'ATR0582G208' => 'atr', 'ATR0705G095' => 'atr', 'Atru.chr1.3514' => 'acertr', 'Atru.chr13.265' => 'acertr', 'Atru.chr6.2730' => 'acertr', 'Atru.chr7.1445' => 'acertr', 'Atru.chr7.2063' => 'acertr', 'AUR62010899' => 'cqu', 'AUR62022188' => 'cqu', 'AUR62022189' => 'cqu', 'AUR62022190' => 'cqu', 'AUR62022191' => 'cqu', 'AUR62022192' => 'cqu', 'AUR62022193' => 'cqu', 'AUR62022194' => 'cqu', 'AUR62022195' => 'cqu', 'AUR62031894' => 'cqu', 'AUR62031895' => 'cqu', 'AUR62031896' => 'cqu', 'AUR62031897' => 'cqu', 'AUR62031898' => 'cqu', 'AUR62031899' => 'cqu', 'AUR62031900' => 'cqu', 'AUR62032534' => 'cqu', 'BcaB02g11027' => 'bca', 'BcaB04g17169' => 'bca', 'BcaB06g25726' => 'bca', 'BcaC01g01307' => 'bca', 'BcaC01g03827' => 'bca', 'BcaC05g28892' => 'bca', 'BcaC08g43370' => 'bca', 'BcaC08g43969' => 'bca', 'BcaC09g48596' => 'bca', 'BcaC09g48597' => 'bca', 'BcaNung00452' => 'bca', 'BcaNung02882' => 'bca', 'BolC1t04770H' => 'bol', 'BolC3t17023H' => 'bol', 'BolC3t17101H' => 'bol', 'BolC3t21365H' => 'bol', 'BolC5t33767H' => 'bol', 'BolC6t35827H' => 'bol', 'BolC6t36540H' => 'bol', 'BolC7t46147H' => 'bol', 'BraA03t13126Z' => 'bra', 'BraA03t14935Z' => 'bra', 'BraA05t20815Z' => 'bra', 'BraA05t22144Z' => 'bra', 'BraA08t32279Z' => 'bra', 'C01p47970' => 'bna', 'C03p48220' => 'bna', 'C03p90440' => 'bna', 'C05p50170' => 'bna', 'C06p07380' => 'bna', 'C06p13680' => 'bna', 'C07p56670' => 'bna', 'CAN.G1124.12' => 'can', 'CAN.G1124.13' => 'can', 'CAN.G1124.14' => 'can', 'CAN.G1124.15' => 'can', 'CAN.G1124.16' => 'can', 'CAN.G1124.5' => 'can', 'CAN.G1349.1' => 'can', 'CAN.G438.1' => 'can', 'CAN.G446.4' => 'can', 'CAN.G446.5' => 'can', 'CANSAT56G1329' => 'cansat', 'CANSAT56G3415' => 'cansat', 'CANSAT56G3966' => 'cansat', 'CARHR042270' => 'chi', 'CARHR091540' => 'chi', 'CARHR236840' => 'chi', 'Carub.0001s4108' => 'cru', 'Carub.0003s1608' => 'cru', 'Carub.0007s1149' => 'cru', 'Ca_01160_v3' => 'car', 'Ca_08233_v3' => 'car', 'Ca_17358_v3' => 'car', 'Ca_23251_v3' => 'car', 'Ca_25561_v3' => 'car', 'Cc04_g02660' => 'ccan', 'Cc06_g10320' => 'ccan', 'CDE05G0443' => 'cde', 'CDE05G1753' => 'cde', 'Cfa003195' => 'cfa', 'Cfa003656' => 'cfa', 'Cfa007137' => 'cfa', 'Ciclev10009423m.g' => 'ccl', 'Ciclev10009617m.g' => 'ccl', 'Ciclev10016745m.g' => 'ccl', 'Ciclev10026493m.g' => 'ccl', 'CiPaw.01G232200' => 'cil', 'CiPaw.02G146200' => 'cil', 'CiPaw.03G226200' => 'cil', 'CiPaw.04G158900' => 'cil', 'ClCG03G016210' => 'cla', 'ClCG05G012470' => 'cla', 'ClCG07G013230' => 'cla', 'ClCG09G000120' => 'cla', 'ClCG11G002230' => 'cla', 'COL.COLO4_13403' => 'col', 'COL.COLO4_20990' => 'col', 'COL.COLO4_30494' => 'col', 'COL.COLO4_34765' => 'col', 'Cpa.g.sc109.12' => 'cpa', 'Cpa.g.sc40.62' => 'cpa', 'CsaV3_2G001980' => 'csa', 'CsaV3_3G020060' => 'csa', 'CsaV3_3G023740' => 'csa', 'CsaV3_7G035360' => 'csa', 'CSS0006885' => 'camsi', 'CSS0010038' => 'camsi', 'CSS0013249' => 'camsi', 'CSS0029495' => 'camsi', 'DCAR_007581' => 'dca', 'DCAR_010471' => 'dca', 'DCAR_012047' => 'dca', 'DCAR_023076' => 'dca', 'DCAR_026349' => 'dca', 'DCAR_027904' => 'dca', 'DCAR_028670' => 'dca', 'DCAR_032098' => 'dca', 'Dinv23382' => 'din', 'Dinv30445' => 'din', 'Dinv36696' => 'din', 'Dinv37985' => 'din', 'Dinv41661' => 'din', 'Duzib150G0752' => 'dzi', 'Duzib160G0537' => 'dzi', 'Duzib168G1228' => 'dzi', 'Duzib187G1193' => 'dzi', 'Duzib192G0172' => 'dzi', 'Duzib235G0070' => 'dzi', 'ECA232G1952' => 'eca', 'ECA232G2558' => 'eca', 'ECA232G4960' => 'eca', 'ECA234G1309' => 'eca', 'ECA247G0347' => 'eca', 'ECA247G0451' => 'eca', 'ECA247G2278' => 'eca', 'ECA247G3519' => 'eca', 'EL10Ac6g13907' => 'bvu', 'EL10Ac8g18399' => 'bvu', 'EL10Ac9g22091' => 'bvu', 'EL10Ac9g22092' => 'bvu', 'EL10Ac9g22093' => 'bvu', 'EL10Ac9g22094' => 'bvu', 'Eucgr.C01005' => 'egr', 'Eucgr.G01913' => 'egr', 'Eucgr.G01914' => 'egr', 'Eucgr.G01915' => 'egr', 'Eucgr.I01569' => 'egr', 'Eucgr.L01394' => 'egr', 'Eucgr.L01395' => 'egr', 'FAN02G1088' => 'fan', 'FAN05G1343' => 'fan', 'FAN09G1467' => 'fan', 'FAN14G1987' => 'fan', 'FAN19G0216' => 'fan', 'FAN23G1180' => 'fan', 'FAN26G1487' => 'fan', 'FAN26G3052' => 'fan', 'FAN28G1130' => 'fan', 'FvH4_1g05960' => 'fve', 'FvH4_6g32270' => 'fve', 'Glyma.01G009000' => 'gma', 'Glyma.02G068100' => 'gma', 'Glyma.07G016300' => 'gma', 'Glyma.08G034400' => 'gma', 'Glyma.08G201700' => 'gma', 'Glyma.13G355100' => 'gma', 'Glyma.15G019100' => 'gma', 'Glyma.16G045300' => 'gma', 'Glyma.16G077400' => 'gma', 'Glyma.16G149600' => 'gma', 'Glyma.19G106400' => 'gma', 'Gohir.A02G118100' => 'ghi', 'Gohir.A05G128800' => 'ghi', 'Gohir.A06G092000' => 'ghi', 'Gohir.A07G008200' => 'ghi', 'Gohir.A10G066400' => 'ghi', 'Gohir.D03G058700' => 'ghi', 'Gohir.D05G133300' => 'ghi', 'Gohir.D06G091500' => 'ghi', 'Gohir.D07G008600' => 'ghi', 'Gohir.D10G067740' => 'ghi', 'Gorai.001G008700' => 'gra', 'Gorai.003G062600' => 'gra', 'Gorai.009G137000' => 'gra', 'Gorai.010G105500' => 'gra', 'Gorai.011G072200' => 'gra', 'GSVIVG01032948001' => 'vvi', 'GSVIVG01035287001' => 'vvi', 'HanXRQChr04g0095921' => 'han', 'HanXRQChr04g0095971' => 'han', 'HanXRQChr06g0168571' => 'han', 'HanXRQChr06g0168581' => 'han', 'HanXRQChr09g0275791' => 'han', 'HanXRQChr09g0275801' => 'han', 'HanXRQChr09g0275811' => 'han', 'HanXRQChr09g0275831' => 'han', 'HanXRQChr09g0275841' => 'han', 'HanXRQChr10g0318331' => 'han', 'HanXRQChr12g0355111' => 'han', 'HanXRQChr16g0501181' => 'han', 'Haze_14986' => 'cav', 'Haze_15838' => 'cav', 'Haze_25811' => 'cav', 'Hma1.2p1_0012F.1_g007330' => 'hma', 'Hma1.2p1_0430F.1_g151480' => 'hma', 'Hma1.2p1_0945F.1_g240300' => 'hma', 'Hma1.2p1_1056F.1_g252660' => 'hma', 'HPP92_008238' => 'vpl', 'HPP92_009089' => 'vpl', 'HPP92_013554' => 'vpl', 'HPP92_021776' => 'vpl', 'HPP92_023417' => 'vpl', 'HPP92_023419' => 'vpl', 'Lalb_Chr05g0223161' => 'lal', 'Lalb_Chr14g0364231' => 'lal', 'Lalb_Chr14g0371811' => 'lal', 'Lalb_Chr14g0373061' => 'lal', 'Lalb_Chr14g0373071' => 'lal', 'Lalb_Chr21g0316991' => 'lal', 'Lalb_Chr22g0351521' => 'lal', 'Lalb_Chr24g0402971' => 'lal', 'Lj1C1173T0' => 'lonja', 'Lj1C1173T1' => 'lonja', 'Lj1g0026347' => 'lja', 'Lj2g0003081' => 'lja', 'Lj2g0027083' => 'lja', 'Lj3g0000765' => 'lja', 'Lj3g0001717' => 'lja', 'Lj3g0011894' => 'lja', 'Lj3g0019121' => 'lja', 'Lj4A393T11' => 'lonja', 'Lj4g0009018' => 'lja', 'Lj5C54T19' => 'lonja', 'Lj9P511T33' => 'lonja', 'Lsat_1_v5_gn_1_37021' => 'lsa', 'Lsat_1_v5_gn_1_37041' => 'lsa', 'Lsat_1_v5_gn_1_37061' => 'lsa', 'Lsat_1_v5_gn_4_100140' => 'lsa', 'Lsat_1_v5_gn_4_100240' => 'lsa', 'Lsat_1_v5_gn_4_100260' => 'lsa', 'Lsat_1_v5_gn_4_100280' => 'lsa', 'Lsat_1_v5_gn_4_100340' => 'lsa', 'Lsat_1_v5_gn_4_100360' => 'lsa', 'Lsat_1_v5_gn_4_100420' => 'lsa', 'Lsat_1_v5_gn_4_100480' => 'lsa', 'Lsat_1_v5_gn_4_99701' => 'lsa', 'Lsat_1_v5_gn_5_144661' => 'lsa', 'Manes.03G025900' => 'mes', 'Manes.03G059800' => 'mes', 'Manes.04G096900' => 'mes', 'Manes.04G133200' => 'mes', 'Manes.11G034500' => 'mes', 'Manes.11G073300' => 'mes', 'Manes.16G074200' => 'mes', 'Manes.16G110200' => 'mes', 'MBI01_g15519_MAGBIO' => 'mbi', 'MBI01_g30455_MAGBIO' => 'mbi', 'MBI04_g06590_MAGBIO' => 'mbi', 'MBI07_g42010_MAGBIO' => 'mbi', 'MBI11_g23198_MAGBIO' => 'mbi', 'MD02G1064200' => 'mdo', 'MD09G1205200' => 'mdo', 'MD15G1091300' => 'mdo', 'MD15G1195000' => 'mdo', 'MD17G1185000' => 'mdo', 'Medtr0016s0050' => 'mtr', 'Medtr0016s0060' => 'mtr', 'Medtr2g101120' => 'mtr', 'Medtr2g101130' => 'mtr', 'Medtr6g088505' => 'mtr', 'Medtr6g088525' => 'mtr', 'Medtr6g088545' => 'mtr', 'Medtr6g088565' => 'mtr', 'Medtr7g084690' => 'mtr', 'Medtr8g014010' => 'mtr', 'Medtr8g014020' => 'mtr', 'Medtr8g014030' => 'mtr', 'Medtr8g102660' => 'mtr', 'MELO3C004582.2' => 'cme', 'MELO3C012987.2' => 'cme', 'MELO3C014759.2' => 'cme', 'MELO3C015403.2' => 'cme', 'MELO3C024444.2' => 'cme', 'Migut.D01002' => 'egut', 'Migut.D01004' => 'egut', 'Migut.I00904' => 'egut', 'Migut.I00905' => 'egut', 'MSTRG.11032' => 'ama', 'MSTRG.11033' => 'ama', 'MSTRG.22644' => 'ama', 'MSTRG.4747' => 'ama', 'MSTRG.4748' => 'ama', 'MSTRG.9483' => 'ama', 'MSTRG.9484' => 'ama', 'Nitab4.5_0000300g0240' => 'nta', 'Nitab4.5_0000300g0280' => 'nta', 'Nitab4.5_0000566g0010' => 'nta', 'Nitab4.5_0001172g0030' => 'nta', 'Nitab4.5_0001172g0040' => 'nta', 'Nitab4.5_0001755g0150' => 'nta', 'Nitab4.5_0003515g0020' => 'nta', 'Nitab4.5_0003515g0030' => 'nta', 'Nitab4.5_0003636g0010' => 'nta', 'Nitab4.5_0007840g0030' => 'nta', 'Nitab4.5_0021917g0010' => 'nta', 'Nn2g10408' => 'nnu', 'Nn4g22074' => 'nnu', 'Nn4g22148' => 'nnu', 'Nn4g23299' => 'nnu', 'Nn8g39098' => 'nnu', 'Oeu017829.1' => 'oeu', 'Oeu026797.1' => 'oeu', 'Oeu042060.1' => 'oeu', 'Oeu050602.1' => 'oeu', 'Oeu053163.1' => 'oeu', 'Oeu060489.1' => 'oeu', 'Oeu063931.1' => 'oeu', 'Oeu063934.1' => 'oeu', 'Oeu063936.1' => 'oeu', 'Oeu064195.1' => 'oeu', 'Os01g0198500' => 'osa', 'Os01g0930500' => 'osa', 'Os02g0229800' => 'osa', 'Os05g0200700' => 'osa', 'Os06g0554600' => 'osa', 'Peaxi162Scf00038g00910' => 'pax', 'Peaxi162Scf00177g00001' => 'pax', 'Peaxi162Scf00177g00002' => 'pax', 'Peaxi162Scf00207g01242' => 'pax', 'Peaxi162Scf00665g00038' => 'pax', 'PGR102G1037' => 'pgr', 'PGR142G2262' => 'pgr', 'PGR142G2343' => 'pgr', 'PGSC0003DMG400000363' => 'stu', 'PGSC0003DMG400002615' => 'stu', 'PGSC0003DMG400016498' => 'stu', 'PGSC0003DMG400016523' => 'stu', 'PGSC0003DMG400016524' => 'stu', 'PGSC0003DMG400016525' => 'stu', 'PGSC0003DMG400016526' => 'stu', 'PGSC0003DMG400026443' => 'stu', 'PGSC0003DMG400026444' => 'stu', 'PGSC0003DMG400026445' => 'stu', 'PGSC0003DMG400026446' => 'stu', 'Phvul.001G098600' => 'pvu', 'Phvul.002G309700' => 'pvu', 'Phvul.004G067900' => 'pvu', 'Phvul.004G170200' => 'pvu', 'Phvul.005G166700' => 'pvu', 'Phvul.010G146000' => 'pvu', 'Potri.001G188900' => 'ptr', 'Potri.003G049800' => 'ptr', 'Potri.006G236700' => 'ptr', 'Potri.014G139900' => 'ptr', 'Potri.018G046500' => 'ptr', 'Potri.018G086500' => 'ptr', 'Prupe.1G446200' => 'ppe', 'Prupe.3G060500' => 'ppe', 'Prupe.7G221500' => 'ppe', 'Psat1g046520' => 'psa', 'Psat3g092840' => 'psa', 'Psat5g296560' => 'psa', 'Psat5g296600' => 'psa', 'Psat5g296640' => 'psa', 'Psat5g296720' => 'psa', 'Psat5g296760' => 'psa', 'Psat5g296800' => 'psa', 'Psat5g296840' => 'psa', 'Psat5g296920' => 'psa', 'Psat7g016000' => 'psa', 'PSO017G4821' => 'pso', 'PSO173G0064' => 'pso', 'PSO173G0102' => 'pso', 'PSO210G5578' => 'pso', 'PSO210G5943' => 'pso', 'PSO478G1201' => 'pso', 'PSO824G0010' => 'pso', 'PSO824G0012' => 'pso', 'PSO824G0020' => 'pso', 'PSO824G0038' => 'pso', 'QL02p042102' => 'qlo', 'QL02p068251' => 'qlo', 'QL05p020368' => 'qlo', 'QL05p020373' => 'qlo', 'RcHm_v2.0_Chr2g0091581' => 'rch', 'RcHm_v2.0_Chr2g0091651' => 'rch', 'RcHm_v2.0_Chr2g0140151' => 'rch', 'Rhsim05G0041000' => 'rsi', 'Rhsim08G0226800' => 'rsi', 'Rhsim12G0202500' => 'rsi', 'Sabra01G0152100' => 'sbr', 'Sabra06G0185000' => 'sbr', 'Sabra18G0045000' => 'sbr', 'Sabra18G0074800' => 'sbr', 'SalBow2G0158' => 'sbo', 'SalBow2G0237' => 'sbo', 'SalBow5G1205' => 'sbo', 'SalBow7G2027' => 'sbo', 'Sc12g0009630' => 'sci', 'Sc12g0009640' => 'sci', 'Sc12g0009650' => 'sci', 'Sc12g0009660' => 'sci', 'Sc12g0009710' => 'sci', 'Sc12g0009720' => 'sci', 'Sc12g0009730' => 'sci', 'Sed0003167' => 'sed', 'Sed0004223' => 'sed', 'Sed0004743' => 'sed', 'Sed0005685' => 'sed', 'Sed0008070' => 'sed', 'Sed0010143' => 'sed', 'Sed0010672' => 'sed', 'Sed0016705' => 'sed', 'Sed0023423' => 'sed', 'Sed0026072' => 'sed', 'SEGI_11031' => 'sgi', 'SEGI_13439' => 'sgi', 'SEGI_15239' => 'sgi', 'SEGI_15713' => 'sgi', 'SEGI_17741' => 'sgi', 'SEGI_22681' => 'sgi', 'SEGI_22892' => 'sgi', 'SGA_v2.0_scaffold4G02019' => 'sas', 'SGA_v2.0_scaffold4G02021' => 'sas', 'SGA_v2.0_scaffold66G22540' => 'sas', 'SGA_v2.0_scaffold66G22541' => 'sas', 'SGA_v2.0_scaffold68G22962' => 'sas', 'SGA_v2.0_scaffold69G23322' => 'sas', 'SGA_v2.0_scaffold69G23324' => 'sas', 'Solyc03g120930.1' => 'sly', 'Solyc06g066490.1' => 'sly', 'Solyc06g066500.1' => 'sly', 'Solyc06g066510.1' => 'sly', 'Solyc06g066520.1' => 'sly', 'Solyc12g008380.1' => 'sly', 'Solyc12g044420.1' => 'sly', 'Sopen03g039760' => 'spe', 'Sopen06g024750' => 'spe', 'Sopen06g024760' => 'spe', 'Sopen06g024770' => 'spe', 'Sopen06g024790' => 'spe', 'Sopen12g003340' => 'spe', 'Sopen12g022730' => 'spe', 'Sopen12g022740' => 'spe', 'Sopen12g022750' => 'spe', 'Sp1g38690' => 'spa', 'Sp3g14700' => 'spa', 'Sp7g27050' => 'spa', 'TAR371G0961' => 'tar', 'TAR383G0743' => 'tar', 'TAR624G0151' => 'tar', 'TAR629G3365' => 'tar', 'THA.LOC104810538' => 'tha', 'THA.LOC104814716' => 'tha', 'THA.LOC104817962' => 'tha', 'THA.LOC104820041' => 'tha', 'Thecc.04G051500' => 'tca', 'Thecc.06G098400' => 'tca', 'Thecc.09G047000' => 'tca', 'Thecc.09G102000' => 'tca', 'Thhalv10011776m.g' => 'esa', 'Thhalv10021537m.g' => 'esa', 'Thhalv10026234m.g' => 'esa', 'TPR.G21370' => 'tpr', 'TPR.G28059' => 'tpr', 'TPR.G31652' => 'tpr', 'TPR.G31655' => 'tpr', 'TPR.G31661' => 'tpr', 'TPR.G31665' => 'tpr', 'TPR.G35013' => 'tpr', 'TPR.G35019' => 'tpr', 'TPR.G37186' => 'tpr', 'TPR.G37192' => 'tpr', 'TWI12G1427' => 'twi', 'TWI18G0227' => 'twi', 'TWI34G1162' => 'twi', 'TWI63G1453' => 'twi', 'TWI81G1099' => 'twi', 'unitig_22.g6004' => 'ugi', 'unitig_32.g11590' => 'ugi', 'unitig_37.g12261' => 'ugi', 'unitig_46.g18561' => 'ugi', 'unitig_736.g22789' => 'ugi', 'unitig_748.g7437' => 'ugi', 'unitig_85.g27212' => 'ugi', 'unitig_88.g27603' => 'ugi', 'unitig_899.g14772' => 'ugi', 'vmacro18859' => 'vma', 'VMungo0251G3636' => 'vmu', 'VMungo0331G1617' => 'vmu', 'VMungo0464G2064' => 'vmu', 'VMungo0464G2151' => 'vmu', 'VMungo1080G0310' => 'vmu', 'VMungo1383G1930' => 'vmu', 'Zm00001eb120430' => 'zma', 'Zm00001eb239500' => 'zma', 'Zm00001eb284070' => 'zma', 'Zm00001eb337950' => 'zma', 'Zm00001eb347290' => 'zma', 'Zm00001eb384670' => 'zma' ) $gf_id = 'HOM05D001131' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001131' ) $data_identifier = 'HOM05D001131' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 3, 'ach' => (int) 5, 'amhyb' => (int) 7, 'aly' => (int) 5, 'aox' => (int) 8, 'arhy' => (int) 4, 'ath' => (int) 3, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 17, 'bca' => (int) 12, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 10, 'cansat' => (int) 3, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 2, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 4, 'cla' => (int) 5, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 4, 'camsi' => (int) 4, 'dca' => (int) 8, 'din' => (int) 5, 'dzi' => (int) 6, 'eca' => (int) 8, 'bvu' => (int) 6, 'egr' => (int) 7, 'fan' => (int) 9, 'fve' => (int) 2, 'gma' => (int) 11, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 12, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 6, 'lal' => (int) 8, 'lonja' => (int) 5, 'lja' => (int) 8, 'lsa' => (int) 13, 'mes' => (int) 8, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 13, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 7, 'nta' => (int) 11, 'nnu' => (int) 5, 'oeu' => (int) 10, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 11, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppe' => (int) 3, 'psa' => (int) 11, 'pso' => (int) 10, 'qlo' => (int) 4, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 7, 'sed' => (int) 10, 'sgi' => (int) 7, 'sas' => (int) 7, 'sly' => (int) 7, 'spe' => (int) 9, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 10, 'twi' => (int) 5, 'ugi' => (int) 9, 'vma' => (int) 1, 'vmu' => (int) 6, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb384670' $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